''If you use this module, please cite the following article: <ref name="Briend 2019">Briend F. et al., A new toolbox to compare target localizations for non-invasive brain stimulation: An application of rTMS treatment for auditory hallucinations in schizophrenia. NeuroImage, Special Issue, submitted</ref>.''

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''If you use this module, please cite the following article: <ref name="Briend 2019">Briend F. et al., A new toolbox to compare target localizations for non-invasive brain stimulation: An application of rTMS treatment for auditory hallucinations in schizophrenia. NeuroImage Clinical, submitted</ref>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.

Module Description

This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.

Terminology

Mesh A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.

Shortest path In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.

10-20 EEG system The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.[2]

Installation

First, open 3D Slicer

Open the Slicer Extensions from the icon on the menu bar

Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.

Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)

Use Cases

The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:

Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.

Surgery measurement.

3D printing.

Panels and their use

Create a mesh

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

Load a volume.nii (by Drag & Drop or the Add Data dialogue).

Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.

Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).

Wait a moment.

Go to Parameters to find the shortest path or Make 10-20 EEG system electrode section.

Parameters to find the shortest path

Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).

Input STL model: The model you use (after "use this mesh", the T1.stl created).

10-20 system electrode

Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear.

4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):

1/ The nasion

2/ The inion

3/ The pre auricular to the left ear

4/ The pre auricular to the right ear

Input STL model: The model you use (after "use this mesh", the T1.stl created).

Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.

The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

Project the stimulation site on the 10-20 system electrode distances and characterize it.

Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.

Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.

Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.

Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.

Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

rTMS resting motor threshold- Correction factor

Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

Localization of the motor hand area via a knob on the precentral gyrus

M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human motor cortex since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the Yousry's method.

Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1.